phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/05_2022/5mps_3539_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/05_2022/5mps_3539.map refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False >& 5mps.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/05_2022/5mps_3539.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/05_2022/5mps_3539.map 3.85
Refinement ran but no refined model file.